After the completion of the human genome sequence, international efforts have been directed to the characterization of the genomes of human-associated resident microbes. The Human Microbiome Project was launched in 2007 with the aim of sequencing the resident microbiota from different sites of the human body. In this paper, we introduce the Human Microbiome Project, the role of the human microbiome in health and disease, and the implications of the microbiome variations in personalized medicine and in pharmacomicrobiomics, which we define as the effect of microbiome variations on drug disposition, action, and toxicity.